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tsoc
openmm
Commits
470c9b7f
Commit
470c9b7f
authored
Jan 27, 2012
by
Mark Friedrichs
Browse files
Renamed math functions in Cuda kernels to single-precision equivalent [cos() -> cosf()]
parent
fed50628
Changes
46
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Inline
Side-by-side
Showing
20 changed files
with
148 additions
and
148 deletions
+148
-148
platforms/cuda/src/kernels/kMonteCarloBarostat.cu
platforms/cuda/src/kernels/kMonteCarloBarostat.cu
+3
-3
platforms/cuda/src/kernels/kRandom.cu
platforms/cuda/src/kernels/kRandom.cu
+6
-6
platforms/cuda/src/kernels/kSettle.cu
platforms/cuda/src/kernels/kSettle.cu
+9
-9
platforms/cuda/src/kernels/rng.cpp
platforms/cuda/src/kernels/rng.cpp
+6
-6
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaFixedEAndGkFields.cu
...cuda/src/kernels/kCalculateAmoebaCudaFixedEAndGkFields.cu
+1
-1
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaGrycuk.cu
.../platforms/cuda/src/kernels/kCalculateAmoebaCudaGrycuk.cu
+5
-5
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu
...latforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu
+1
-1
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.cu
...rms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.cu
+3
-3
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff_b.h
...ms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff_b.h
+3
-3
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood_b.h
...atforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood_b.h
+1
-1
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaLocalForces.cu
...forms/cuda/src/kernels/kCalculateAmoebaCudaLocalForces.cu
+19
-19
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPME.cu
...eba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPME.cu
+5
-5
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.cu
...src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.cu
+21
-21
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostaticF2P.h
...c/kernels/kCalculateAmoebaCudaPmeDirectElectrostaticF2P.h
+4
-4
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostaticT2.h
...rc/kernels/kCalculateAmoebaCudaPmeDirectElectrostaticT2.h
+1
-1
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
...ms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
+6
-6
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.cu
.../src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.cu
+12
-12
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaVdw14_7.h
.../platforms/cuda/src/kernels/kCalculateAmoebaCudaVdw14_7.h
+6
-6
plugins/amoeba/platforms/cuda/src/kernels/kFindInteractingBlocksVdw.h
...ba/platforms/cuda/src/kernels/kFindInteractingBlocksVdw.h
+6
-6
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateCDLJObcGbsaSoftcoreForces1.h
...s/cuda/src/kernels/kCalculateCDLJObcGbsaSoftcoreForces1.h
+30
-30
No files found.
platforms/cuda/src/kernels/kMonteCarloBarostat.cu
View file @
470c9b7f
...
@@ -57,9 +57,9 @@ __global__ void kScaleAtomCoordinates_kernel(float scale, int numMolecules, floa
...
@@ -57,9 +57,9 @@ __global__ void kScaleAtomCoordinates_kernel(float scale, int numMolecules, floa
// Move it into the first periodic box.
// Move it into the first periodic box.
int
xcell
=
(
int
)
floor
(
center
.
x
*
invPeriodicBoxSize
.
x
);
int
xcell
=
(
int
)
floor
f
(
center
.
x
*
invPeriodicBoxSize
.
x
);
int
ycell
=
(
int
)
floor
(
center
.
y
*
invPeriodicBoxSize
.
y
);
int
ycell
=
(
int
)
floor
f
(
center
.
y
*
invPeriodicBoxSize
.
y
);
int
zcell
=
(
int
)
floor
(
center
.
z
*
invPeriodicBoxSize
.
z
);
int
zcell
=
(
int
)
floor
f
(
center
.
z
*
invPeriodicBoxSize
.
z
);
float3
delta
=
make_float3
(
xcell
*
periodicBoxSize
.
x
,
ycell
*
periodicBoxSize
.
y
,
zcell
*
periodicBoxSize
.
z
);
float3
delta
=
make_float3
(
xcell
*
periodicBoxSize
.
x
,
ycell
*
periodicBoxSize
.
y
,
zcell
*
periodicBoxSize
.
z
);
center
.
x
-=
delta
.
x
;
center
.
x
-=
delta
.
x
;
center
.
y
-=
delta
.
y
;
center
.
y
-=
delta
.
y
;
...
...
platforms/cuda/src/kernels/kRandom.cu
View file @
470c9b7f
...
@@ -94,7 +94,7 @@ void kGenerateRandoms_kernel()
...
@@ -94,7 +94,7 @@ void kGenerateRandoms_kernel()
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
<<
5
;
state
.
y
^=
state
.
y
<<
5
;
x1
=
sqrt
(
-
2.0
f
*
log
(
x1
));
x1
=
sqrt
f
(
-
2.0
f
*
log
f
(
x1
));
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
state
.
z
=
state
.
w
;
state
.
z
=
state
.
w
;
...
@@ -106,7 +106,7 @@ void kGenerateRandoms_kernel()
...
@@ -106,7 +106,7 @@ void kGenerateRandoms_kernel()
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
<<
5
;
state
.
y
^=
state
.
y
<<
5
;
sRand
[
pos1
].
x
=
x1
*
cos
(
2.0
f
*
3.14159265
f
*
x2
);
sRand
[
pos1
].
x
=
x1
*
cos
f
(
2.0
f
*
3.14159265
f
*
x2
);
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
state
.
z
=
state
.
w
;
state
.
z
=
state
.
w
;
...
@@ -117,7 +117,7 @@ void kGenerateRandoms_kernel()
...
@@ -117,7 +117,7 @@ void kGenerateRandoms_kernel()
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
<<
5
;
state
.
y
^=
state
.
y
<<
5
;
x3
=
sqrt
(
-
2.0
f
*
log
(
x3
));
x3
=
sqrt
f
(
-
2.0
f
*
log
f
(
x3
));
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
state
.
z
=
state
.
w
;
state
.
z
=
state
.
w
;
...
@@ -129,7 +129,7 @@ void kGenerateRandoms_kernel()
...
@@ -129,7 +129,7 @@ void kGenerateRandoms_kernel()
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
<<
5
;
state
.
y
^=
state
.
y
<<
5
;
sRand
[
pos1
].
y
=
x3
*
cos
(
2.0
f
*
3.14159265
f
*
x4
);
sRand
[
pos1
].
y
=
x3
*
cos
f
(
2.0
f
*
3.14159265
f
*
x4
);
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
state
.
z
=
state
.
w
;
state
.
z
=
state
.
w
;
...
@@ -140,14 +140,14 @@ void kGenerateRandoms_kernel()
...
@@ -140,14 +140,14 @@ void kGenerateRandoms_kernel()
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
<<
13
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
>>
17
;
state
.
y
^=
state
.
y
<<
5
;
state
.
y
^=
state
.
y
<<
5
;
x5
=
sqrt
(
-
2.0
f
*
log
(
x5
));
x5
=
sqrt
f
(
-
2.0
f
*
log
f
(
x5
));
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
k
=
(
state
.
z
>>
2
)
+
(
state
.
w
>>
3
)
+
(
carry
>>
2
);
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
m
=
state
.
w
+
state
.
w
+
state
.
z
+
carry
;
state
.
z
=
state
.
w
;
state
.
z
=
state
.
w
;
state
.
w
=
m
;
state
.
w
=
m
;
carry
=
k
>>
30
;
carry
=
k
>>
30
;
float
x6
=
(
float
)(
state
.
x
+
state
.
y
+
state
.
w
)
/
(
float
)
0xffffffff
;
float
x6
=
(
float
)(
state
.
x
+
state
.
y
+
state
.
w
)
/
(
float
)
0xffffffff
;
sRand
[
pos1
].
z
=
x5
*
cos
(
2.0
f
*
3.14159265
f
*
x6
);
sRand
[
pos1
].
z
=
x5
*
cos
f
(
2.0
f
*
3.14159265
f
*
x6
);
pos1
+=
blockDim
.
x
;
pos1
+=
blockDim
.
x
;
}
}
...
...
platforms/cuda/src/kernels/kSettle.cu
View file @
470c9b7f
...
@@ -131,9 +131,9 @@ void kApplySettle_kernel()
...
@@ -131,9 +131,9 @@ void kApplySettle_kernel()
float
yaksYd
=
zaksZd
*
xaksXd
-
xaksZd
*
zaksXd
;
float
yaksYd
=
zaksZd
*
xaksXd
-
xaksZd
*
zaksXd
;
float
zaksYd
=
xaksZd
*
yaksXd
-
yaksZd
*
xaksXd
;
float
zaksYd
=
xaksZd
*
yaksXd
-
yaksZd
*
xaksXd
;
float
axlng
=
sqrt
(
xaksXd
*
xaksXd
+
yaksXd
*
yaksXd
+
zaksXd
*
zaksXd
);
float
axlng
=
sqrt
f
(
xaksXd
*
xaksXd
+
yaksXd
*
yaksXd
+
zaksXd
*
zaksXd
);
float
aylng
=
sqrt
(
xaksYd
*
xaksYd
+
yaksYd
*
yaksYd
+
zaksYd
*
zaksYd
);
float
aylng
=
sqrt
f
(
xaksYd
*
xaksYd
+
yaksYd
*
yaksYd
+
zaksYd
*
zaksYd
);
float
azlng
=
sqrt
(
xaksZd
*
xaksZd
+
yaksZd
*
yaksZd
+
zaksZd
*
zaksZd
);
float
azlng
=
sqrt
f
(
xaksZd
*
xaksZd
+
yaksZd
*
yaksZd
+
zaksZd
*
zaksZd
);
float
trns11
=
xaksXd
/
axlng
;
float
trns11
=
xaksXd
/
axlng
;
float
trns21
=
yaksXd
/
axlng
;
float
trns21
=
yaksXd
/
axlng
;
float
trns31
=
zaksXd
/
axlng
;
float
trns31
=
zaksXd
/
axlng
;
...
@@ -159,13 +159,13 @@ void kApplySettle_kernel()
...
@@ -159,13 +159,13 @@ void kApplySettle_kernel()
// --- Step2 A2' ---
// --- Step2 A2' ---
float
rc
=
0.5
f
*
params
.
y
;
float
rc
=
0.5
f
*
params
.
y
;
float
rb
=
sqrt
(
params
.
x
*
params
.
x
-
rc
*
rc
);
float
rb
=
sqrt
f
(
params
.
x
*
params
.
x
-
rc
*
rc
);
float
ra
=
rb
*
(
m1
+
m2
)
/
totalMass
;
float
ra
=
rb
*
(
m1
+
m2
)
/
totalMass
;
rb
-=
ra
;
rb
-=
ra
;
float
sinphi
=
za1d
/
ra
;
float
sinphi
=
za1d
/
ra
;
float
cosphi
=
sqrt
(
1.0
f
-
sinphi
*
sinphi
);
float
cosphi
=
sqrt
f
(
1.0
f
-
sinphi
*
sinphi
);
float
sinpsi
=
(
zb1d
-
zc1d
)
/
(
2
*
rc
*
cosphi
);
float
sinpsi
=
(
zb1d
-
zc1d
)
/
(
2
*
rc
*
cosphi
);
float
cospsi
=
sqrt
(
1.0
f
-
sinpsi
*
sinpsi
);
float
cospsi
=
sqrt
f
(
1.0
f
-
sinpsi
*
sinpsi
);
float
ya2d
=
ra
*
cosphi
;
float
ya2d
=
ra
*
cosphi
;
float
xb2d
=
-
rc
*
cospsi
;
float
xb2d
=
-
rc
*
cospsi
;
...
@@ -173,7 +173,7 @@ void kApplySettle_kernel()
...
@@ -173,7 +173,7 @@ void kApplySettle_kernel()
float
yc2d
=
-
rb
*
cosphi
+
rc
*
sinpsi
*
sinphi
;
float
yc2d
=
-
rb
*
cosphi
+
rc
*
sinpsi
*
sinphi
;
float
xb2d2
=
xb2d
*
xb2d
;
float
xb2d2
=
xb2d
*
xb2d
;
float
hh2
=
4.0
f
*
xb2d2
+
(
yb2d
-
yc2d
)
*
(
yb2d
-
yc2d
)
+
(
zb1d
-
zc1d
)
*
(
zb1d
-
zc1d
);
float
hh2
=
4.0
f
*
xb2d2
+
(
yb2d
-
yc2d
)
*
(
yb2d
-
yc2d
)
+
(
zb1d
-
zc1d
)
*
(
zb1d
-
zc1d
);
float
deltx
=
2.0
f
*
xb2d
+
sqrt
(
4.0
f
*
xb2d2
-
hh2
+
params
.
y
*
params
.
y
);
float
deltx
=
2.0
f
*
xb2d
+
sqrt
f
(
4.0
f
*
xb2d2
-
hh2
+
params
.
y
*
params
.
y
);
xb2d
-=
deltx
*
0.5
f
;
xb2d
-=
deltx
*
0.5
f
;
// --- Step3 al,be,ga ---
// --- Step3 al,be,ga ---
...
@@ -183,11 +183,11 @@ void kApplySettle_kernel()
...
@@ -183,11 +183,11 @@ void kApplySettle_kernel()
float
gama
=
xb0d
*
yb1d
-
xb1d
*
yb0d
+
xc0d
*
yc1d
-
xc1d
*
yc0d
;
float
gama
=
xb0d
*
yb1d
-
xb1d
*
yb0d
+
xc0d
*
yc1d
-
xc1d
*
yc0d
;
float
al2be2
=
alpa
*
alpa
+
beta
*
beta
;
float
al2be2
=
alpa
*
alpa
+
beta
*
beta
;
float
sinthe
=
(
alpa
*
gama
-
beta
*
sqrt
(
al2be2
-
gama
*
gama
)
)
/
al2be2
;
float
sinthe
=
(
alpa
*
gama
-
beta
*
sqrt
f
(
al2be2
-
gama
*
gama
)
)
/
al2be2
;
// --- Step4 A3' ---
// --- Step4 A3' ---
float
costhe
=
sqrt
(
1.0
f
-
sinthe
*
sinthe
);
float
costhe
=
sqrt
f
(
1.0
f
-
sinthe
*
sinthe
);
float
xa3d
=
-
ya2d
*
sinthe
;
float
xa3d
=
-
ya2d
*
sinthe
;
float
ya3d
=
ya2d
*
costhe
;
float
ya3d
=
ya2d
*
costhe
;
float
za3d
=
za1d
;
float
za3d
=
za1d
;
...
...
platforms/cuda/src/kernels/rng.cpp
View file @
470c9b7f
...
@@ -96,7 +96,7 @@ void RNG::zigset()
...
@@ -96,7 +96,7 @@ void RNG::zigset()
wn
[
0
]
=
q
/
m1
;
wn
[
127
]
=
tn
/
m1
;
wn
[
0
]
=
q
/
m1
;
wn
[
127
]
=
tn
/
m1
;
fn
[
0
]
=
1.
;
fn
[
127
]
=
exp
(
-
.5
*
tn
*
tn
);
fn
[
0
]
=
1.
;
fn
[
127
]
=
exp
(
-
.5
*
tn
*
tn
);
for
(
uint
i
=
126
;
i
>
0
;
i
--
)
{
for
(
uint
i
=
126
;
i
>
0
;
i
--
)
{
const
double
dn
=
sqrt
(
-
2
*
log
(
vn
/
tn
+
exp
(
-
.5
*
tn
*
tn
)));
const
double
dn
=
sqrt
f
(
-
2
*
log
(
vn
/
tn
+
exp
(
-
.5
*
tn
*
tn
)));
kn
[
i
+
1
]
=
ULONG32
((
dn
/
tn
)
*
m1
);
kn
[
i
+
1
]
=
ULONG32
((
dn
/
tn
)
*
m1
);
fn
[
i
]
=
exp
(
-
.5
*
dn
*
dn
);
fn
[
i
]
=
exp
(
-
.5
*
dn
*
dn
);
wn
[
i
]
=
dn
/
m1
;
wn
[
i
]
=
dn
/
m1
;
...
@@ -130,7 +130,7 @@ double RNG::gamma(double shape, double scale)
...
@@ -130,7 +130,7 @@ double RNG::gamma(double shape, double scale)
return
gamma
(
shape
+
1.
,
scale
)
*
pow
(
rand_open01
(),
1.0
/
shape
);
return
gamma
(
shape
+
1.
,
scale
)
*
pow
(
rand_open01
(),
1.0
/
shape
);
const
double
d
=
shape
-
1.
/
3.
;
const
double
d
=
shape
-
1.
/
3.
;
const
double
c
=
1.
/
sqrt
(
9.
*
d
);
const
double
c
=
1.
/
sqrt
f
(
9.
*
d
);
double
x
,
v
;
double
x
,
v
;
for
(;;)
{
for
(;;)
{
do
{
do
{
...
@@ -186,7 +186,7 @@ int RNG::poisson(double mu)
...
@@ -186,7 +186,7 @@ int RNG::poisson(double mu)
if
(
big_mu
)
{
if
(
big_mu
)
{
new_big_mu
=
1
;
new_big_mu
=
1
;
muprev
=
mu
;
muprev
=
mu
;
s
=
sqrt
(
mu
);
s
=
sqrt
f
(
mu
);
d
=
6.
*
mu
*
mu
;
d
=
6.
*
mu
*
mu
;
big_l
=
floor
(
mu
-
1.1484
);
big_l
=
floor
(
mu
-
1.1484
);
}
}
...
@@ -240,7 +240,7 @@ int RNG::poisson(double mu)
...
@@ -240,7 +240,7 @@ int RNG::poisson(double mu)
if
(
new_big_mu
||
mu
!=
muprev2
)
{
if
(
new_big_mu
||
mu
!=
muprev2
)
{
muprev2
=
mu
;
muprev2
=
mu
;
omega
=
1.0
/
(
sqrt
(
2.0
*
PI
)
*
s
);
omega
=
1.0
/
(
sqrt
f
(
2.0
*
PI
)
*
s
);
b1
=
one_24
/
mu
;
b1
=
one_24
/
mu
;
b2
=
0.3
*
b1
*
b1
;
b2
=
0.3
*
b1
*
b1
;
c3
=
one_7
*
b1
*
b2
;
c3
=
one_7
*
b1
*
b2
;
...
@@ -280,7 +280,7 @@ Step_F:
...
@@ -280,7 +280,7 @@ Step_F:
-
del
;
-
del
;
else
else
px
=
fk
*
log
(
1.
+
v
)
-
difmuk
-
del
;
px
=
fk
*
log
(
1.
+
v
)
-
difmuk
-
del
;
py
=
1.0
/
(
sqrt
(
2.0
*
PI
)
*
sqrt
(
fk
));
py
=
1.0
/
(
sqrt
f
(
2.0
*
PI
)
*
sqrt
f
(
fk
));
}
}
x
=
(
0.5
-
difmuk
)
/
s
;
x
=
(
0.5
-
difmuk
)
/
s
;
x
*=
x
;
/* x^2 */
x
*=
x
;
/* x^2 */
...
@@ -332,7 +332,7 @@ int RNG::binomial(double pp, int n)
...
@@ -332,7 +332,7 @@ int RNG::binomial(double pp, int n)
m
=
(
int
)
ffm
;
m
=
(
int
)
ffm
;
fm
=
m
;
fm
=
m
;
npq
=
np
*
q
;
npq
=
np
*
q
;
p1
=
(
int
)(
2.195
*
sqrt
(
npq
)
-
4.6
*
q
)
+
0.5
;
p1
=
(
int
)(
2.195
*
sqrt
f
(
npq
)
-
4.6
*
q
)
+
0.5
;
xm
=
fm
+
0.5
;
xm
=
fm
+
0.5
;
xl
=
xm
-
p1
;
xl
=
xm
-
p1
;
xr
=
xm
+
p1
;
xr
=
xm
+
p1
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaFixedEAndGkFields.cu
View file @
470c9b7f
...
@@ -156,7 +156,7 @@ __device__ void calculateFixedGkFieldPairIxn_kernel( float4 atomCoordinatesI,
...
@@ -156,7 +156,7 @@ __device__ void calculateFixedGkFieldPairIxn_kernel( float4 atomCoordinatesI,
qyzk
=
labFrameQuadrupoleJ
[
5
];
qyzk
=
labFrameQuadrupoleJ
[
5
];
qzzk
=
labFrameQuadrupoleJ
[
8
];
qzzk
=
labFrameQuadrupoleJ
[
8
];
expterm
=
exp
(
-
r2
/
(
gkc
*
rb2
));
expterm
=
exp
f
(
-
r2
/
(
gkc
*
rb2
));
expc
=
expterm
/
gkc
;
expc
=
expterm
/
gkc
;
dexpc
=
-
2.0
f
/
(
gkc
*
rb2
);
dexpc
=
-
2.0
f
/
(
gkc
*
rb2
);
gf2
=
1.0
f
/
(
r2
+
rb2
*
expterm
);
gf2
=
1.0
f
/
(
r2
+
rb2
*
expterm
);
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaGrycuk.cu
View file @
470c9b7f
...
@@ -105,7 +105,7 @@ __device__ void calculateGrycukBornRadiiPairIxn_kernel( GrycukParticle& atomI, G
...
@@ -105,7 +105,7 @@ __device__ void calculateGrycukBornRadiiPairIxn_kernel( GrycukParticle& atomI, G
zr
=
atomJ
.
z
-
atomI
.
z
;
zr
=
atomJ
.
z
-
atomI
.
z
;
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
r
=
sqrt
(
r2
);
r
=
sqrt
f
(
r2
);
sk
=
atomJ
.
scaledRadius
;
sk
=
atomJ
.
scaledRadius
;
sk2
=
sk
*
sk
;
sk2
=
sk
*
sk
;
...
@@ -170,7 +170,7 @@ void kReduceGrycukGbsaBornSum_kernel()
...
@@ -170,7 +170,7 @@ void kReduceGrycukGbsaBornSum_kernel()
float
radius
=
cSim
.
pObcData
[
pos
].
x
;
float
radius
=
cSim
.
pObcData
[
pos
].
x
;
radius
=
1.0
f
/
(
radius
*
radius
*
radius
);
radius
=
1.0
f
/
(
radius
*
radius
*
radius
);
sum
=
radius
-
sum
;
sum
=
radius
-
sum
;
sum
=
sum
<=
0.0
f
?
1000.0
f
:
pow
(
sum
,
-
1.0
f
/
3.0
f
);
sum
=
sum
<=
0.0
f
?
1000.0
f
:
pow
f
(
sum
,
-
1.0
f
/
3.0
f
);
cSim
.
pBornRadii
[
pos
]
=
sum
;
cSim
.
pBornRadii
[
pos
]
=
sum
;
pos
+=
gridDim
.
x
*
blockDim
.
x
;
pos
+=
gridDim
.
x
*
blockDim
.
x
;
...
@@ -305,9 +305,9 @@ __device__ void calculateGrycukChainRulePairIxn_kernel( GrycukChainRuleParticle&
...
@@ -305,9 +305,9 @@ __device__ void calculateGrycukChainRulePairIxn_kernel( GrycukChainRuleParticle&
float
lik
,
uik
;
float
lik
,
uik
;
float
lik4
,
uik4
;
float
lik4
,
uik4
;
float
factor
=
-
pow
(
pi
,
third
)
*
pow
(
6.0
f
,(
2.0
f
*
third
))
/
9.0
f
;
float
factor
=
-
pow
f
(
pi
,
third
)
*
pow
f
(
6.0
f
,(
2.0
f
*
third
))
/
9.0
f
;
float
term
=
pi43
/
(
atomI
.
bornRadius
*
atomI
.
bornRadius
*
atomI
.
bornRadius
);
float
term
=
pi43
/
(
atomI
.
bornRadius
*
atomI
.
bornRadius
*
atomI
.
bornRadius
);
term
=
factor
/
pow
(
term
,
(
4.0
f
*
third
)
);
term
=
factor
/
pow
f
(
term
,
(
4.0
f
*
third
)
);
float
xr
=
atomJ
.
x
-
atomI
.
x
;
float
xr
=
atomJ
.
x
-
atomI
.
x
;
float
yr
=
atomJ
.
y
-
atomI
.
y
;
float
yr
=
atomJ
.
y
-
atomI
.
y
;
...
@@ -316,7 +316,7 @@ __device__ void calculateGrycukChainRulePairIxn_kernel( GrycukChainRuleParticle&
...
@@ -316,7 +316,7 @@ __device__ void calculateGrycukChainRulePairIxn_kernel( GrycukChainRuleParticle&
float
sk
=
atomJ
.
scaledRadius
;
float
sk
=
atomJ
.
scaledRadius
;
float
sk2
=
sk
*
sk
;
float
sk2
=
sk
*
sk
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
float
r
=
sqrt
(
r2
);
float
r
=
sqrt
f
(
r2
);
float
de
=
0.0
f
;
float
de
=
0.0
f
;
if
(
(
atomI
.
radius
+
r
)
<
sk
){
if
(
(
atomI
.
radius
+
r
)
<
sk
){
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu
View file @
470c9b7f
...
@@ -172,7 +172,7 @@ __device__ void calculateKirkwoodPairIxnOrig_kernel( KirkwoodParticle& atomI,
...
@@ -172,7 +172,7 @@ __device__ void calculateKirkwoodPairIxnOrig_kernel( KirkwoodParticle& atomI,
dexpcr
=
2.0
f
/
(
cAmoebaSim
.
gkc
*
rb2
*
rb2
);
dexpcr
=
2.0
f
/
(
cAmoebaSim
.
gkc
*
rb2
*
rb2
);
dgfdr
=
0.5
f
*
expterm
*
(
1.0
f
+
r2
/
(
rb2
*
cAmoebaSim
.
gkc
));
dgfdr
=
0.5
f
*
expterm
*
(
1.0
f
+
r2
/
(
rb2
*
cAmoebaSim
.
gkc
));
gf2
=
1.0
f
/
(
r2
+
rb2
*
expterm
);
gf2
=
1.0
f
/
(
r2
+
rb2
*
expterm
);
gf
=
sqrt
(
gf2
);
gf
=
sqrt
f
(
gf2
);
gf3
=
gf2
*
gf
;
gf3
=
gf2
*
gf
;
gf5
=
gf3
*
gf2
;
gf5
=
gf3
*
gf2
;
gf7
=
gf5
*
gf2
;
gf7
=
gf5
*
gf2
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.cu
View file @
470c9b7f
...
@@ -186,9 +186,9 @@ __device__ void calculateKirkwoodEDiffPairIxnOrig_kernel( KirkwoodEDiffParticle&
...
@@ -186,9 +186,9 @@ __device__ void calculateKirkwoodEDiffPairIxnOrig_kernel( KirkwoodEDiffParticle&
scale7
=
1.0
f
-
(
1.0
f
-
damp
+
0.6
f
*
damp2
)
*
dampE
;
scale7
=
1.0
f
-
(
1.0
f
-
damp
+
0.6
f
*
damp2
)
*
dampE
;
//scale9 = 1.0f - (1.0f - damp + (18.0f*damp2 - (9.0f*damp*damp2))/35.0f)*dampE;
//scale9 = 1.0f - (1.0f - damp + (18.0f*damp2 - (9.0f*damp*damp2))/35.0f)*dampE;
ddsc3_1
=
-
3.0
f
*
damp
*
exp
(
damp
)
*
xr
/
r2
;
ddsc3_1
=
-
3.0
f
*
damp
*
exp
f
(
damp
)
*
xr
/
r2
;
ddsc3_2
=
-
3.0
f
*
damp
*
exp
(
damp
)
*
yr
/
r2
;
ddsc3_2
=
-
3.0
f
*
damp
*
exp
f
(
damp
)
*
yr
/
r2
;
ddsc3_3
=
-
3.0
f
*
damp
*
exp
(
damp
)
*
zr
/
r2
;
ddsc3_3
=
-
3.0
f
*
damp
*
exp
f
(
damp
)
*
zr
/
r2
;
ddsc5_1
=
-
damp
*
ddsc3_1
;
ddsc5_1
=
-
damp
*
ddsc3_1
;
ddsc5_2
=
-
damp
*
ddsc3_2
;
ddsc5_2
=
-
damp
*
ddsc3_2
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff_b.h
View file @
470c9b7f
...
@@ -69,9 +69,9 @@ __device__ void SUB_METHOD_NAME( calculateKirkwoodEDiffPairIxn, _kernel)( Kirkwo
...
@@ -69,9 +69,9 @@ __device__ void SUB_METHOD_NAME( calculateKirkwoodEDiffPairIxn, _kernel)( Kirkwo
scale7
=
1
.
0
f
-
(
1
.
0
f
-
damp
+
0
.
6
f
*
damp2
)
*
dampE
;
scale7
=
1
.
0
f
-
(
1
.
0
f
-
damp
+
0
.
6
f
*
damp2
)
*
dampE
;
#ifdef F1
#ifdef F1
ddsc3_1
=
-
3
.
0
f
*
damp
*
exp
(
damp
)
*
xr
*
rr2
*
rr3
;
ddsc3_1
=
-
3
.
0
f
*
damp
*
exp
f
(
damp
)
*
xr
*
rr2
*
rr3
;
ddsc3_2
=
-
3
.
0
f
*
damp
*
exp
(
damp
)
*
yr
*
rr2
*
rr3
;
ddsc3_2
=
-
3
.
0
f
*
damp
*
exp
f
(
damp
)
*
yr
*
rr2
*
rr3
;
ddsc3_3
=
-
3
.
0
f
*
damp
*
exp
(
damp
)
*
zr
*
rr2
*
rr3
;
ddsc3_3
=
-
3
.
0
f
*
damp
*
exp
f
(
damp
)
*
zr
*
rr2
*
rr3
;
ddsc5_1
=
-
3
.
0
f
*
damp
*
ddsc3_1
*
rr2
;
ddsc5_1
=
-
3
.
0
f
*
damp
*
ddsc3_1
*
rr2
;
ddsc5_2
=
-
3
.
0
f
*
damp
*
ddsc3_2
*
rr2
;
ddsc5_2
=
-
3
.
0
f
*
damp
*
ddsc3_2
*
rr2
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood_b.h
View file @
470c9b7f
...
@@ -51,7 +51,7 @@ static __device__ void SUB_METHOD_NAME( calculateKirkwoodPairIxn, _kernel)( Kirk
...
@@ -51,7 +51,7 @@ static __device__ void SUB_METHOD_NAME( calculateKirkwoodPairIxn, _kernel)( Kirk
float
dgfdr
=
0
.
5
f
*
expterm
*
(
1
.
0
f
+
r2
/
(
rb2
*
cAmoebaSim
.
gkc
));
float
dgfdr
=
0
.
5
f
*
expterm
*
(
1
.
0
f
+
r2
/
(
rb2
*
cAmoebaSim
.
gkc
));
float
gf2
=
1
.
0
f
/
(
r2
+
rb2
*
expterm
);
float
gf2
=
1
.
0
f
/
(
r2
+
rb2
*
expterm
);
float
gf
=
sqrt
(
gf2
);
float
gf
=
sqrt
f
(
gf2
);
float
gf3
=
gf2
*
gf
;
float
gf3
=
gf2
*
gf
;
float
gf5
=
gf3
*
gf2
;
float
gf5
=
gf3
*
gf2
;
float
gf7
=
gf5
*
gf2
;
float
gf7
=
gf5
*
gf2
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaLocalForces.cu
View file @
470c9b7f
...
@@ -320,7 +320,7 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -320,7 +320,7 @@ void kCalculateAmoebaLocalForces_kernel()
float
dy
=
atomB
.
y
-
atomA
.
y
;
float
dy
=
atomB
.
y
-
atomA
.
y
;
float
dz
=
atomB
.
z
-
atomA
.
z
;
float
dz
=
atomB
.
z
-
atomA
.
z
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r
=
sqrt
(
r2
);
float
r
=
sqrt
f
(
r2
);
float
deltaIdeal
=
r
-
bond
.
x
;
float
deltaIdeal
=
r
-
bond
.
x
;
#if defined OLD
#if defined OLD
energy
+=
0.5
f
*
bond
.
y
*
deltaIdeal
*
deltaIdeal
;
energy
+=
0.5
f
*
bond
.
y
*
deltaIdeal
*
deltaIdeal
;
...
@@ -382,16 +382,16 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -382,16 +382,16 @@ void kCalculateAmoebaLocalForces_kernel()
float3
cp
;
float3
cp
;
CROSS_PRODUCT
(
v0
,
v1
,
cp
);
CROSS_PRODUCT
(
v0
,
v1
,
cp
);
float
rp
=
DOT3
(
cp
,
cp
);
//cx * cx + cy * cy + cz * cz;
float
rp
=
DOT3
(
cp
,
cp
);
//cx * cx + cy * cy + cz * cz;
rp
=
max
(
sqrt
(
rp
),
1.0e-06
f
);
rp
=
max
(
sqrt
f
(
rp
),
1.0e-06
f
);
float
r21
=
DOT3
(
v0
,
v0
);
// dx1 * dx1 + dy1 * dy1 + dz1 * dz1;
float
r21
=
DOT3
(
v0
,
v0
);
// dx1 * dx1 + dy1 * dy1 + dz1 * dz1;
float
r23
=
DOT3
(
v1
,
v1
);
// dx2 * dx2 + dy2 * dy2 + dz2 * dz2;
float
r23
=
DOT3
(
v1
,
v1
);
// dx2 * dx2 + dy2 * dy2 + dz2 * dz2;
float
dot
=
DOT3
(
v0
,
v1
);
// dx1 * dx2 + dy1 * dy2 + dz1 * dz2;
float
dot
=
DOT3
(
v0
,
v1
);
// dx1 * dx2 + dy1 * dy2 + dz1 * dz2;
float
cosine
=
dot
/
sqrt
(
r21
*
r23
);
float
cosine
=
dot
/
sqrt
f
(
r21
*
r23
);
// e = angunit * force * dt2 * (1.0d0+cang*dt+qang*dt2+pang*dt3+sang*dt4)
// e = angunit * force * dt2 * (1.0d0+cang*dt+qang*dt2+pang*dt3+sang*dt4)
// deddt = angunit * force * dt * radian * (2.0d0 + 3.0d0*cang*dt + 4.0d0*qang*dt2 + 5.0d0*pang*dt3 + 6.0d0*sang*dt4)
// deddt = angunit * force * dt * radian * (2.0d0 + 3.0d0*cang*dt + 4.0d0*qang*dt2 + 5.0d0*pang*dt3 + 6.0d0*sang*dt4)
float
angle
=
acos
(
cosine
);
float
angle
=
acos
f
(
cosine
);
float
deltaIdeal
=
angle
*
(
180.0
f
/
LOCAL_HACK_PI
)
-
bond_angle1
.
x
;
float
deltaIdeal
=
angle
*
(
180.0
f
/
LOCAL_HACK_PI
)
-
bond_angle1
.
x
;
float
deltaIdeal2
=
deltaIdeal
*
deltaIdeal
;
float
deltaIdeal2
=
deltaIdeal
*
deltaIdeal
;
float
deltaIdeal3
=
deltaIdeal
*
deltaIdeal2
;
float
deltaIdeal3
=
deltaIdeal
*
deltaIdeal2
;
...
@@ -507,7 +507,7 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -507,7 +507,7 @@ void kCalculateAmoebaLocalForces_kernel()
float
cosine
=
product
>
0.0
f
?
(
dot
/
product
)
:
0.0
f
;
float
cosine
=
product
>
0.0
f
?
(
dot
/
product
)
:
0.0
f
;
cosine
=
cosine
>
1.0
f
?
1.0
f
:
cosine
;
cosine
=
cosine
>
1.0
f
?
1.0
f
:
cosine
;
cosine
=
cosine
<
-
1.0
f
?
-
1.0
f
:
cosine
;
cosine
=
cosine
<
-
1.0
f
?
-
1.0
f
:
cosine
;
float
angle
=
acos
(
cosine
);
float
angle
=
acos
f
(
cosine
);
// if product == 0, set force/energy to 0
// if product == 0, set force/energy to 0
...
@@ -670,19 +670,19 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -670,19 +670,19 @@ void kCalculateAmoebaLocalForces_kernel()
float
v1
=
torsionParam1
.
x
;
float
v1
=
torsionParam1
.
x
;
float
angle
=
torsionParam1
.
y
;
float
angle
=
torsionParam1
.
y
;
float
c1
=
cos
(
angle
);
float
c1
=
cos
f
(
angle
);
float
s1
=
sin
(
angle
);
float
s1
=
sin
f
(
angle
);
float
v2
=
torsionParam1
.
z
;
float
v2
=
torsionParam1
.
z
;
angle
=
torsionParam1
.
w
;
angle
=
torsionParam1
.
w
;
float
c2
=
cos
(
angle
);
float
c2
=
cos
f
(
angle
);
float
s2
=
sin
(
angle
);
float
s2
=
sin
f
(
angle
);
float
v3
=
torsionParam2
.
x
;
float
v3
=
torsionParam2
.
x
;
angle
=
torsionParam2
.
y
;
angle
=
torsionParam2
.
y
;
float
c3
=
cos
(
angle
);
float
c3
=
cos
f
(
angle
);
float
s3
=
sin
(
angle
);
float
s3
=
sin
f
(
angle
);
// compute the multiple angle trigonometry and the phase terms
// compute the multiple angle trigonometry and the phase terms
...
@@ -857,7 +857,7 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -857,7 +857,7 @@ void kCalculateAmoebaLocalForces_kernel()
float
ru2
=
xu
*
xu
+
yu
*
yu
+
zu
*
zu
;
float
ru2
=
xu
*
xu
+
yu
*
yu
+
zu
*
zu
;
float
rtru
=
sqrtf
(
rt2
*
ru2
);
float
rtru
=
sqrtf
(
rt2
*
ru2
);
float
rdc
=
sqrt
(
xdc
*
xdc
+
ydc
*
ydc
+
zdc
*
zdc
);
float
rdc
=
sqrt
f
(
xdc
*
xdc
+
ydc
*
ydc
+
zdc
*
zdc
);
float
cosine
=
rtru
>
0.0
f
?
(
xt
*
xu
+
yt
*
yu
+
zt
*
zu
)
/
rtru
:
0.0
f
;
float
cosine
=
rtru
>
0.0
f
?
(
xt
*
xu
+
yt
*
yu
+
zt
*
zu
)
/
rtru
:
0.0
f
;
float
sine
=
(
rtru
*
rdc
)
>
0.0
f
?
(
xdc
*
xtu
+
ydc
*
ytu
+
zdc
*
ztu
)
/
(
rdc
*
rtru
)
:
0.0
f
;
float
sine
=
(
rtru
*
rdc
)
>
0.0
f
?
(
xdc
*
xtu
+
ydc
*
ytu
+
zdc
*
ztu
)
/
(
rdc
*
rtru
)
:
0.0
f
;
...
@@ -1020,13 +1020,13 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -1020,13 +1020,13 @@ void kCalculateAmoebaLocalForces_kernel()
float
yp
=
zcb
*
xab
-
xcb
*
zab
;
float
yp
=
zcb
*
xab
-
xcb
*
zab
;
float
zp
=
xcb
*
yab
-
ycb
*
xab
;
float
zp
=
xcb
*
yab
-
ycb
*
xab
;
float
rp
=
sqrt
(
xp
*
xp
+
yp
*
yp
+
zp
*
zp
);
float
rp
=
sqrt
f
(
xp
*
xp
+
yp
*
yp
+
zp
*
zp
);
float
dot
=
xab
*
xcb
+
yab
*
ycb
+
zab
*
zcb
;
float
dot
=
xab
*
xcb
+
yab
*
ycb
+
zab
*
zcb
;
float
cosine
=
rab
*
rcb
>
0.0
f
?
(
dot
/
(
rab
*
rcb
))
:
1.0
f
;
float
cosine
=
rab
*
rcb
>
0.0
f
?
(
dot
/
(
rab
*
rcb
))
:
1.0
f
;
cosine
=
cosine
>
1.0
f
?
1.0
f
:
cosine
;
cosine
=
cosine
>
1.0
f
?
1.0
f
:
cosine
;
cosine
=
cosine
<
-
1.0
f
?
-
1.0
f
:
cosine
;
cosine
=
cosine
<
-
1.0
f
?
-
1.0
f
:
cosine
;
float
angle
=
acos
(
cosine
);
float
angle
=
acos
f
(
cosine
);
// find chain rule terms for the bond angle deviation
// find chain rule terms for the bond angle deviation
...
@@ -1158,9 +1158,9 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -1158,9 +1158,9 @@ void kCalculateAmoebaLocalForces_kernel()
float
adXcd_nrm2
=
adXcd_0
*
adXcd_0
+
adXcd_1
*
adXcd_1
+
adXcd_2
*
adXcd_2
;
float
adXcd_nrm2
=
adXcd_0
*
adXcd_0
+
adXcd_1
*
adXcd_1
+
adXcd_2
*
adXcd_2
;
float
adXcd_dot_db
=
xdb
*
adXcd_0
+
ydb
*
adXcd_1
+
zdb
*
adXcd_2
;
float
adXcd_dot_db
=
xdb
*
adXcd_0
+
ydb
*
adXcd_1
+
zdb
*
adXcd_2
;
adXcd_dot_db
/=
sqrt
(
rdb2
*
adXcd_nrm2
);
adXcd_dot_db
/=
sqrt
f
(
rdb2
*
adXcd_nrm2
);
float
angle
=
abs
(
asin
(
adXcd_dot_db
)
);
float
angle
=
abs
(
asin
f
(
adXcd_dot_db
)
);
// find the out-of-plane energy and master chain rule terms
// find the out-of-plane energy and master chain rule terms
...
@@ -1327,7 +1327,7 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -1327,7 +1327,7 @@ void kCalculateAmoebaLocalForces_kernel()
cosine1
=
cosine1
>
1.0
f
?
1.0
f
:
cosine1
;
cosine1
=
cosine1
>
1.0
f
?
1.0
f
:
cosine1
;
cosine1
=
cosine1
<
-
1.0
f
?
-
1.0
f
:
cosine1
;
cosine1
=
cosine1
<
-
1.0
f
?
-
1.0
f
:
cosine1
;
float
angle1
=
LOCAL_HACK_RADIAN
*
acos
(
cosine1
);
float
angle1
=
LOCAL_HACK_RADIAN
*
acos
f
(
cosine1
);
float
sign
=
xba
*
xu
+
yba
*
yu
+
zba
*
zu
;
float
sign
=
xba
*
xu
+
yba
*
yu
+
zba
*
zu
;
angle1
=
sign
<
0.0
f
?
-
angle1
:
angle1
;
angle1
=
sign
<
0.0
f
?
-
angle1
:
angle1
;
float
value1
=
angle1
;
float
value1
=
angle1
;
...
@@ -1336,7 +1336,7 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -1336,7 +1336,7 @@ void kCalculateAmoebaLocalForces_kernel()
float
cosine2
=
(
xu
*
xv
+
yu
*
yv
+
zu
*
zv
)
/
rurv
;
float
cosine2
=
(
xu
*
xv
+
yu
*
yv
+
zu
*
zv
)
/
rurv
;
cosine2
=
cosine2
>
1.0
f
?
1.0
f
:
cosine2
;
cosine2
=
cosine2
>
1.0
f
?
1.0
f
:
cosine2
;
cosine2
=
cosine2
<
-
1.0
f
?
-
1.0
f
:
cosine2
;
cosine2
=
cosine2
<
-
1.0
f
?
-
1.0
f
:
cosine2
;
float
angle2
=
LOCAL_HACK_RADIAN
*
acos
(
cosine2
);
float
angle2
=
LOCAL_HACK_RADIAN
*
acos
f
(
cosine2
);
sign
=
xcb
*
xv
+
ycb
*
yv
+
zcb
*
zv
;
sign
=
xcb
*
xv
+
ycb
*
yv
+
zcb
*
zv
;
angle2
=
sign
<
0.0
f
?
-
angle2
:
angle2
;
angle2
=
sign
<
0.0
f
?
-
angle2
:
angle2
;
...
@@ -1577,7 +1577,7 @@ void kCalculateAmoebaLocalForces_kernel()
...
@@ -1577,7 +1577,7 @@ void kCalculateAmoebaLocalForces_kernel()
float
dz
=
atomB
.
z
-
atomA
.
z
;
float
dz
=
atomB
.
z
-
atomA
.
z
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r
=
sqrt
(
r2
);
float
r
=
sqrt
f
(
r2
);
float
deltaIdeal
=
r
-
bond
.
x
;
float
deltaIdeal
=
r
-
bond
.
x
;
float
deltaIdeal2
=
deltaIdeal
*
deltaIdeal
;
float
deltaIdeal2
=
deltaIdeal
*
deltaIdeal
;
energy
+=
bond
.
y
*
deltaIdeal2
*
(
1.0
f
+
cAmoebaSim
.
amoebaUreyBradleyCubicParameter
*
deltaIdeal
+
energy
+=
bond
.
y
*
deltaIdeal2
*
(
1.0
f
+
cAmoebaSim
.
amoebaUreyBradleyCubicParameter
*
deltaIdeal
+
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPME.cu
View file @
470c9b7f
...
@@ -137,9 +137,9 @@ void kComputeAmoebaBsplines_kernel()
...
@@ -137,9 +137,9 @@ void kComputeAmoebaBsplines_kernel()
for
(
int
i
=
blockIdx
.
x
*
blockDim
.
x
+
threadIdx
.
x
;
i
<
cSim
.
atoms
;
i
+=
blockDim
.
x
*
gridDim
.
x
)
{
for
(
int
i
=
blockIdx
.
x
*
blockDim
.
x
+
threadIdx
.
x
;
i
<
cSim
.
atoms
;
i
+=
blockDim
.
x
*
gridDim
.
x
)
{
float4
posq
=
cSim
.
pPosq
[
i
];
float4
posq
=
cSim
.
pPosq
[
i
];
posq
.
x
-=
floor
(
posq
.
x
*
cSim
.
invPeriodicBoxSizeX
)
*
cSim
.
periodicBoxSizeX
;
posq
.
x
-=
floor
f
(
posq
.
x
*
cSim
.
invPeriodicBoxSizeX
)
*
cSim
.
periodicBoxSizeX
;
posq
.
y
-=
floor
(
posq
.
y
*
cSim
.
invPeriodicBoxSizeY
)
*
cSim
.
periodicBoxSizeY
;
posq
.
y
-=
floor
f
(
posq
.
y
*
cSim
.
invPeriodicBoxSizeY
)
*
cSim
.
periodicBoxSizeY
;
posq
.
z
-=
floor
(
posq
.
z
*
cSim
.
invPeriodicBoxSizeZ
)
*
cSim
.
periodicBoxSizeZ
;
posq
.
z
-=
floor
f
(
posq
.
z
*
cSim
.
invPeriodicBoxSizeZ
)
*
cSim
.
periodicBoxSizeZ
;
// First axis.
// First axis.
...
@@ -210,7 +210,7 @@ void kFindAmoebaAtomRangeForGrid_kernel()
...
@@ -210,7 +210,7 @@ void kFindAmoebaAtomRangeForGrid_kernel()
// some work in the charge spreading kernel.
// some work in the charge spreading kernel.
float
posz
=
cSim
.
pPosq
[
atomData
.
x
].
z
;
float
posz
=
cSim
.
pPosq
[
atomData
.
x
].
z
;
posz
-=
floor
(
posz
*
cSim
.
invPeriodicBoxSizeZ
)
*
cSim
.
periodicBoxSizeZ
;
posz
-=
floor
f
(
posz
*
cSim
.
invPeriodicBoxSizeZ
)
*
cSim
.
periodicBoxSizeZ
;
float
w
=
posz
*
cSim
.
invPeriodicBoxSizeZ
;
float
w
=
posz
*
cSim
.
invPeriodicBoxSizeZ
;
float
fr
=
cSim
.
pmeGridSize
.
z
*
(
w
-
(
int
)(
w
+
0.5
f
)
+
0.5
f
);
float
fr
=
cSim
.
pmeGridSize
.
z
*
(
w
-
(
int
)(
w
+
0.5
f
)
+
0.5
f
);
int
z
=
((
int
)
fr
)
-
AMOEBA_PME_ORDER
+
1
;
int
z
=
((
int
)
fr
)
-
AMOEBA_PME_ORDER
+
1
;
...
@@ -449,7 +449,7 @@ void kAmoebaReciprocalConvolution_kernel()
...
@@ -449,7 +449,7 @@ void kAmoebaReciprocalConvolution_kernel()
cuComplex
grid
=
cSim
.
pPmeGrid
[
index
];
cuComplex
grid
=
cSim
.
pPmeGrid
[
index
];
float
m2
=
mhx
*
mhx
+
mhy
*
mhy
+
mhz
*
mhz
;
float
m2
=
mhx
*
mhx
+
mhy
*
mhy
+
mhz
*
mhz
;
float
denom
=
m2
*
bx
*
by
*
bz
;
float
denom
=
m2
*
bx
*
by
*
bz
;
float
eterm
=
scaleFactor
*
exp
(
-
expFactor
*
m2
)
/
denom
;
float
eterm
=
scaleFactor
*
exp
f
(
-
expFactor
*
m2
)
/
denom
;
cSim
.
pPmeGrid
[
index
]
=
make_cuComplex
(
grid
.
x
*
eterm
,
grid
.
y
*
eterm
);
cSim
.
pPmeGrid
[
index
]
=
make_cuComplex
(
grid
.
x
*
eterm
,
grid
.
y
*
eterm
);
}
}
}
}
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.cu
View file @
470c9b7f
...
@@ -192,10 +192,10 @@ __device__ void calculateBn_kernel( float r, float4* bn, float* bn0, float *bn5
...
@@ -192,10 +192,10 @@ __device__ void calculateBn_kernel( float r, float4* bn, float* bn0, float *bn5
if
(
cSim
.
alphaEwald
>
0.0
f
){
if
(
cSim
.
alphaEwald
>
0.0
f
){
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
}
}
float
exp2a
=
exp
(
-
(
ralpha
*
ralpha
));
float
exp2a
=
exp
f
(
-
(
ralpha
*
ralpha
));
float
rr1
=
1.0
f
/
r
;
float
rr1
=
1.0
f
/
r
;
*
bn0
=
erfc
(
ralpha
)
*
rr1
;
*
bn0
=
erfc
f
(
ralpha
)
*
rr1
;
float
rr2
=
rr1
*
rr1
;
float
rr2
=
rr1
*
rr1
;
alsq2n
*=
alsq2
;
alsq2n
*=
alsq2
;
...
@@ -241,14 +241,14 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrig_kernel( const PmeDire
...
@@ -241,14 +241,14 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrig_kernel( const PmeDire
// periodic box
// periodic box
xr
-=
floor
(
xr
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
xr
-=
floor
f
(
xr
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
yr
-=
floor
(
yr
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
yr
-=
floor
f
(
yr
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
zr
-=
floor
(
zr
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
zr
-=
floor
f
(
zr
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
float
r
=
sqrt
(
r2
);
float
r
=
sqrt
f
(
r2
);
float
ck
=
atomJ
.
q
;
float
ck
=
atomJ
.
q
;
// set the permanent multipole and induced dipole values;
// set the permanent multipole and induced dipole values;
...
@@ -282,14 +282,14 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrig_kernel( const PmeDire
...
@@ -282,14 +282,14 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrig_kernel( const PmeDire
// calculate the real space error function terms
// calculate the real space error function terms
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
bn0
=
erfc
(
ralpha
)
/
r
;
float
bn0
=
erfc
f
(
ralpha
)
/
r
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2n
=
0.0
f
;
float
alsq2n
=
0.0
f
;
if
(
cSim
.
alphaEwald
>
0.0
f
){
if
(
cSim
.
alphaEwald
>
0.0
f
){
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
}
}
float
exp2a
=
exp
(
-
(
ralpha
*
ralpha
));
float
exp2a
=
exp
f
(
-
(
ralpha
*
ralpha
));
alsq2n
*=
alsq2
;
alsq2n
*=
alsq2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
...
@@ -336,7 +336,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrig_kernel( const PmeDire
...
@@ -336,7 +336,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrig_kernel( const PmeDire
float
ratio
=
r
/
damp
;
float
ratio
=
r
/
damp
;
damp
=
-
pgamma
*
ratio
*
ratio
*
ratio
;
damp
=
-
pgamma
*
ratio
*
ratio
*
ratio
;
if
(
damp
>
-
50.0
f
){
if
(
damp
>
-
50.0
f
){
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
scale3
=
1.0
f
-
expdamp
;
scale3
=
1.0
f
-
expdamp
;
scale5
=
1.0
f
-
(
1.0
f
-
damp
)
*
expdamp
;
scale5
=
1.0
f
-
(
1.0
f
-
damp
)
*
expdamp
;
scale7
=
1.0
f
-
(
1.0
f
-
damp
+
0.6
f
*
damp
*
damp
)
*
expdamp
;
scale7
=
1.0
f
-
(
1.0
f
-
damp
+
0.6
f
*
damp
*
damp
)
*
expdamp
;
...
@@ -957,16 +957,16 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
...
@@ -957,16 +957,16 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
// periodic box
// periodic box
delta
.
x
-=
floor
(
delta
.
x
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
delta
.
x
-=
floor
f
(
delta
.
x
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
delta
.
y
-=
floor
(
delta
.
y
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
delta
.
y
-=
floor
f
(
delta
.
y
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
delta
.
z
-=
floor
(
delta
.
z
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
delta
.
z
-=
floor
f
(
delta
.
z
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
delta
.
w
=
delta
.
x
*
delta
.
x
+
delta
.
y
*
delta
.
y
+
delta
.
z
*
delta
.
z
;
delta
.
w
=
delta
.
x
*
delta
.
x
+
delta
.
y
*
delta
.
y
+
delta
.
z
*
delta
.
z
;
if
(
delta
.
w
>
cSim
.
nonbondedCutoffSqr
){
if
(
delta
.
w
>
cSim
.
nonbondedCutoffSqr
){
return
;
return
;
}
}
float
r
=
sqrt
(
delta
.
w
);
float
r
=
sqrt
f
(
delta
.
w
);
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
...
@@ -974,11 +974,11 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
...
@@ -974,11 +974,11 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
if
(
cSim
.
alphaEwald
>
0.0
f
){
if
(
cSim
.
alphaEwald
>
0.0
f
){
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
}
}
float
exp2a
=
exp
(
-
(
ralpha
*
ralpha
));
float
exp2a
=
exp
f
(
-
(
ralpha
*
ralpha
));
float
rr1
=
1.0
f
/
r
;
float
rr1
=
1.0
f
/
r
;
delta
.
w
=
rr1
;
delta
.
w
=
rr1
;
float
bn0
=
erfc
(
ralpha
)
*
rr1
;
float
bn0
=
erfc
f
(
ralpha
)
*
rr1
;
*
energy
+=
forceFactor
*
atomI
.
q
*
atomJ
.
q
*
bn0
;
*
energy
+=
forceFactor
*
atomI
.
q
*
atomJ
.
q
*
bn0
;
float
rr2
=
rr1
*
rr1
;
float
rr2
=
rr1
*
rr1
;
alsq2n
*=
alsq2
;
alsq2n
*=
alsq2
;
...
@@ -1058,16 +1058,16 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrigg_kernel( PmeDirectEle
...
@@ -1058,16 +1058,16 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrigg_kernel( PmeDirectEle
// periodic box
// periodic box
delta
.
x
-=
floor
(
delta
.
x
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
delta
.
x
-=
floor
f
(
delta
.
x
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
delta
.
y
-=
floor
(
delta
.
y
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
delta
.
y
-=
floor
f
(
delta
.
y
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
delta
.
z
-=
floor
(
delta
.
z
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
delta
.
z
-=
floor
f
(
delta
.
z
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
delta
.
w
=
delta
.
x
*
delta
.
x
+
delta
.
y
*
delta
.
y
+
delta
.
z
*
delta
.
z
;
delta
.
w
=
delta
.
x
*
delta
.
x
+
delta
.
y
*
delta
.
y
+
delta
.
z
*
delta
.
z
;
if
(
delta
.
w
>
cSim
.
nonbondedCutoffSqr
){
if
(
delta
.
w
>
cSim
.
nonbondedCutoffSqr
){
return
;
return
;
}
}
float
r
=
sqrt
(
delta
.
w
);
float
r
=
sqrt
f
(
delta
.
w
);
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
...
@@ -1075,11 +1075,11 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrigg_kernel( PmeDirectEle
...
@@ -1075,11 +1075,11 @@ __device__ void calculatePmeDirectElectrostaticPairIxnOrigg_kernel( PmeDirectEle
if
(
cSim
.
alphaEwald
>
0.0
f
){
if
(
cSim
.
alphaEwald
>
0.0
f
){
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
}
}
float
exp2a
=
exp
(
-
(
ralpha
*
ralpha
));
float
exp2a
=
exp
f
(
-
(
ralpha
*
ralpha
));
float
rr1
=
1.0
f
/
r
;
float
rr1
=
1.0
f
/
r
;
delta
.
w
=
rr1
;
delta
.
w
=
rr1
;
float
bn0
=
erfc
(
ralpha
)
*
rr1
;
float
bn0
=
erfc
f
(
ralpha
)
*
rr1
;
*
energy
+=
forceFactor
*
atomI
.
q
*
atomJ
.
q
*
bn0
;
*
energy
+=
forceFactor
*
atomI
.
q
*
atomJ
.
q
*
bn0
;
float
rr2
=
rr1
*
rr1
;
float
rr2
=
rr1
*
rr1
;
alsq2n
*=
alsq2
;
alsq2n
*=
alsq2
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostaticF2P.h
View file @
470c9b7f
...
@@ -41,7 +41,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
...
@@ -41,7 +41,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
damp
=
damp
<
-
50
.
0
f
?
0
.
0
f
:
damp
;
damp
=
damp
<
-
50
.
0
f
?
0
.
0
f
:
damp
;
}
}
float
scale5
=
(
damp
==
0
.
0
f
)
?
1
.
0
f
:
(
1
.
0
f
-
(
1
.
0
f
-
damp
)
*
exp
(
damp
));
float
scale5
=
(
damp
==
0
.
0
f
)
?
1
.
0
f
:
(
1
.
0
f
-
(
1
.
0
f
-
damp
)
*
exp
f
(
damp
));
float
rr5
=
rr1
*
rr1
;
float
rr5
=
rr1
*
rr1
;
rr5
=
3
.
0
f
*
rr1
*
rr5
*
rr5
;
rr5
=
3
.
0
f
*
rr1
*
rr5
*
rr5
;
#ifdef APPLY_SCALE
#ifdef APPLY_SCALE
...
@@ -79,7 +79,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
...
@@ -79,7 +79,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
ftm23
+=
(
qiuk3
+
qiukp3
)
*
psc5
;
ftm23
+=
(
qiuk3
+
qiukp3
)
*
psc5
;
#endif
#endif
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
float
scale3
=
(
damp
==
0
.
0
f
)
?
1
.
0
f
:
(
1
.
0
f
-
expdamp
);
float
scale3
=
(
damp
==
0
.
0
f
)
?
1
.
0
f
:
(
1
.
0
f
-
expdamp
);
float
rr3
=
rr1
*
rr1
*
rr1
;
float
rr3
=
rr1
*
rr1
*
rr1
;
...
@@ -190,7 +190,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
...
@@ -190,7 +190,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
if
(
damp
!=
0
.
0
f
){
if
(
damp
!=
0
.
0
f
){
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
float
temp3
=
-
1
.
5
f
*
damp
*
expdamp
*
rr1
*
rr1
;
float
temp3
=
-
1
.
5
f
*
damp
*
expdamp
*
rr1
*
rr1
;
float
temp5
=
-
damp
;
float
temp5
=
-
damp
;
float
temp7
=
-
0
.
2
f
-
0
.
6
f
*
damp
;
float
temp7
=
-
0
.
2
f
-
0
.
6
f
*
damp
;
...
@@ -395,7 +395,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
...
@@ -395,7 +395,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnF2
if
(
damp
!=
0
.
0
f
){
if
(
damp
!=
0
.
0
f
){
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
float
temp3
=
-
1
.
5
f
*
damp
*
expdamp
*
rr1
*
rr1
;
float
temp3
=
-
1
.
5
f
*
damp
*
expdamp
*
rr1
*
rr1
;
float
temp5
=
-
damp
;
float
temp5
=
-
damp
;
float
temp7
=
-
0
.
2
f
-
0
.
6
f
*
damp
;
float
temp7
=
-
0
.
2
f
-
0
.
6
f
*
damp
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostaticT2.h
View file @
470c9b7f
...
@@ -42,7 +42,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnT2
...
@@ -42,7 +42,7 @@ static __device__ void SUB_METHOD_NAME( calculatePmeDirectElectrostaticPairIxnT2
float
ratio
=
1
.
0
f
/
(
rr1
*
damp
);
float
ratio
=
1
.
0
f
/
(
rr1
*
damp
);
damp
=
-
pgamma
*
ratio
*
ratio
*
ratio
;
damp
=
-
pgamma
*
ratio
*
ratio
*
ratio
;
if
(
damp
>
-
50
.
0
f
){
if
(
damp
>
-
50
.
0
f
){
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
scale3
=
1
.
0
f
-
expdamp
;
scale3
=
1
.
0
f
-
expdamp
;
scale5
=
1
.
0
f
-
(
1
.
0
f
-
damp
)
*
expdamp
;
scale5
=
1
.
0
f
-
(
1
.
0
f
-
damp
)
*
expdamp
;
scale7
=
1
.
0
f
-
(
1
.
0
f
-
damp
+
0
.
6
f
*
damp
*
damp
)
*
expdamp
;
scale7
=
1
.
0
f
-
(
1
.
0
f
-
damp
+
0
.
6
f
*
damp
*
damp
)
*
expdamp
;
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
View file @
470c9b7f
...
@@ -201,9 +201,9 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
...
@@ -201,9 +201,9 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
// periodic boundary conditions
// periodic boundary conditions
xr
-=
floor
(
xr
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
xr
-=
floor
f
(
xr
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
yr
-=
floor
(
yr
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
yr
-=
floor
f
(
yr
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
zr
-=
floor
(
zr
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
zr
-=
floor
f
(
zr
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
...
@@ -214,10 +214,10 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
...
@@ -214,10 +214,10 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
bn0
=
erfc
(
ralpha
)
/
r
;
float
bn0
=
erfc
f
(
ralpha
)
/
r
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
float
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
float
exp2a
=
exp
(
-
(
ralpha
*
ralpha
));
float
exp2a
=
exp
f
(
-
(
ralpha
*
ralpha
));
alsq2n
*=
alsq2
;
alsq2n
*=
alsq2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
...
@@ -243,7 +243,7 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
...
@@ -243,7 +243,7 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
damp
=
-
pgamma
*
ratio
;
damp
=
-
pgamma
*
ratio
;
if
(
damp
>
-
50.0
f
)
{
if
(
damp
>
-
50.0
f
)
{
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
scale3
=
1.0
f
-
expdamp
;
scale3
=
1.0
f
-
expdamp
;
scale5
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
);
scale5
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
);
scale7
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
+
(
0.6
f
*
damp
*
damp
));
scale7
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
+
(
0.6
f
*
damp
*
damp
));
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.cu
View file @
470c9b7f
...
@@ -85,9 +85,9 @@ __device__ void setupMutualInducedFieldPairIxn_kernel( const MutualInducedPartic
...
@@ -85,9 +85,9 @@ __device__ void setupMutualInducedFieldPairIxn_kernel( const MutualInducedPartic
// pdelta->xiodic boundary conditions
// pdelta->xiodic boundary conditions
delta
->
x
-=
floor
(
delta
->
x
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
delta
->
x
-=
floor
f
(
delta
->
x
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
delta
->
y
-=
floor
(
delta
->
y
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
delta
->
y
-=
floor
f
(
delta
->
y
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
delta
->
z
-=
floor
(
delta
->
z
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
delta
->
z
-=
floor
f
(
delta
->
z
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
float
r2
=
(
delta
->
x
*
delta
->
x
)
+
(
delta
->
y
*
delta
->
y
)
+
(
delta
->
z
*
delta
->
z
);
float
r2
=
(
delta
->
x
*
delta
->
x
)
+
(
delta
->
y
*
delta
->
y
)
+
(
delta
->
z
*
delta
->
z
);
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
...
@@ -97,10 +97,10 @@ __device__ void setupMutualInducedFieldPairIxn_kernel( const MutualInducedPartic
...
@@ -97,10 +97,10 @@ __device__ void setupMutualInducedFieldPairIxn_kernel( const MutualInducedPartic
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
bn0
=
erfc
(
ralpha
)
/
r
;
float
bn0
=
erfc
f
(
ralpha
)
/
r
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
float
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
float
exp2a
=
exp
(
-
(
ralpha
*
ralpha
));
float
exp2a
=
exp
f
(
-
(
ralpha
*
ralpha
));
alsq2n
*=
alsq2
;
alsq2n
*=
alsq2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
...
@@ -120,7 +120,7 @@ __device__ void setupMutualInducedFieldPairIxn_kernel( const MutualInducedPartic
...
@@ -120,7 +120,7 @@ __device__ void setupMutualInducedFieldPairIxn_kernel( const MutualInducedPartic
damp
=
-
pgamma
*
ratio
;
damp
=
-
pgamma
*
ratio
;
if
(
damp
>
-
50.0
f
)
{
if
(
damp
>
-
50.0
f
)
{
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
scale3
=
1.0
f
-
expdamp
;
scale3
=
1.0
f
-
expdamp
;
scale5
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
);
scale5
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
);
}
}
...
@@ -171,9 +171,9 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
...
@@ -171,9 +171,9 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
// periodic boundary conditions
// periodic boundary conditions
xr
-=
floor
(
xr
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
xr
-=
floor
f
(
xr
*
cSim
.
invPeriodicBoxSizeX
+
0.5
f
)
*
cSim
.
periodicBoxSizeX
;
yr
-=
floor
(
yr
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
yr
-=
floor
f
(
yr
*
cSim
.
invPeriodicBoxSizeY
+
0.5
f
)
*
cSim
.
periodicBoxSizeY
;
zr
-=
floor
(
zr
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
zr
-=
floor
f
(
zr
*
cSim
.
invPeriodicBoxSizeZ
+
0.5
f
)
*
cSim
.
periodicBoxSizeZ
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
float
r2
=
xr
*
xr
+
yr
*
yr
+
zr
*
zr
;
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
if
(
r2
<=
cSim
.
nonbondedCutoffSqr
){
...
@@ -183,10 +183,10 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
...
@@ -183,10 +183,10 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
ralpha
=
cSim
.
alphaEwald
*
r
;
float
bn0
=
erfc
(
ralpha
)
/
r
;
float
bn0
=
erfc
f
(
ralpha
)
/
r
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2
=
2.0
f
*
cSim
.
alphaEwald
*
cSim
.
alphaEwald
;
float
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
float
alsq2n
=
1.0
f
/
(
cAmoebaSim
.
sqrtPi
*
cSim
.
alphaEwald
);
float
exp2a
=
exp
(
-
(
ralpha
*
ralpha
));
float
exp2a
=
exp
f
(
-
(
ralpha
*
ralpha
));
alsq2n
*=
alsq2
;
alsq2n
*=
alsq2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
float
bn1
=
(
bn0
+
alsq2n
*
exp2a
)
/
r2
;
...
@@ -206,7 +206,7 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
...
@@ -206,7 +206,7 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
damp
=
-
pgamma
*
ratio
;
damp
=
-
pgamma
*
ratio
;
if
(
damp
>
-
50.0
f
)
{
if
(
damp
>
-
50.0
f
)
{
float
expdamp
=
exp
(
damp
);
float
expdamp
=
exp
f
(
damp
);
scale3
=
1.0
f
-
expdamp
;
scale3
=
1.0
f
-
expdamp
;
scale5
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
);
scale5
=
1.0
f
-
expdamp
*
(
1.0
f
-
damp
);
}
}
...
...
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaVdw14_7.h
View file @
470c9b7f
...
@@ -117,9 +117,9 @@ void METHOD_NAME(kCalculateAmoebaVdw14_7, _kernel)(
...
@@ -117,9 +117,9 @@ void METHOD_NAME(kCalculateAmoebaVdw14_7, _kernel)(
ijForce
[
2
]
=
psA
[
j
].
z
-
localParticle
.
z
;
ijForce
[
2
]
=
psA
[
j
].
z
-
localParticle
.
z
;
if
(
cAmoebaSim
.
vdwUsePBC
)
if
(
cAmoebaSim
.
vdwUsePBC
)
{
{
ijForce
[
0
]
-=
floor
(
ijForce
[
0
]
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
ijForce
[
0
]
-=
floor
f
(
ijForce
[
0
]
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
ijForce
[
1
]
-=
floor
(
ijForce
[
1
]
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
ijForce
[
1
]
-=
floor
f
(
ijForce
[
1
]
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
ijForce
[
2
]
-=
floor
(
ijForce
[
2
]
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
ijForce
[
2
]
-=
floor
f
(
ijForce
[
2
]
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
}
}
float
energy
;
float
energy
;
...
@@ -211,9 +211,9 @@ flags = 0xFFFFFFFF;
...
@@ -211,9 +211,9 @@ flags = 0xFFFFFFFF;
ijForce
[
2
]
=
psA
[
jIdx
].
z
-
localParticle
.
z
;
ijForce
[
2
]
=
psA
[
jIdx
].
z
-
localParticle
.
z
;
if
(
cAmoebaSim
.
vdwUsePBC
)
if
(
cAmoebaSim
.
vdwUsePBC
)
{
{
ijForce
[
0
]
-=
floor
(
ijForce
[
0
]
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
ijForce
[
0
]
-=
floor
f
(
ijForce
[
0
]
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
ijForce
[
1
]
-=
floor
(
ijForce
[
1
]
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
ijForce
[
1
]
-=
floor
f
(
ijForce
[
1
]
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
ijForce
[
2
]
-=
floor
(
ijForce
[
2
]
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
ijForce
[
2
]
-=
floor
f
(
ijForce
[
2
]
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
}
}
calculateVdw14_7PairIxn_kernel
(
combindedSigma
,
combindedEpsilon
,
ijForce
,
&
energy
);
calculateVdw14_7PairIxn_kernel
(
combindedSigma
,
combindedEpsilon
,
ijForce
,
&
energy
);
...
...
plugins/amoeba/platforms/cuda/src/kernels/kFindInteractingBlocksVdw.h
View file @
470c9b7f
...
@@ -47,9 +47,9 @@ __global__ void METHOD_NAME(kFindBlocksWithInteractionsVdw, _kernel)()
...
@@ -47,9 +47,9 @@ __global__ void METHOD_NAME(kFindBlocksWithInteractionsVdw, _kernel)()
float
dy
=
centera
.
y
-
centerb
.
y
;
float
dy
=
centera
.
y
-
centerb
.
y
;
float
dz
=
centera
.
z
-
centerb
.
z
;
float
dz
=
centera
.
z
-
centerb
.
z
;
#ifdef USE_PERIODIC
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dx
-=
floor
f
(
dx
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dy
-=
floor
f
(
dy
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
dz
-=
floor
f
(
dz
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
#endif
float4
boxSizea
=
cSim
.
pGridBoundingBox
[
x
];
float4
boxSizea
=
cSim
.
pGridBoundingBox
[
x
];
float4
boxSizeb
=
cSim
.
pGridBoundingBox
[
y
];
float4
boxSizeb
=
cSim
.
pGridBoundingBox
[
y
];
...
@@ -108,9 +108,9 @@ __global__ void METHOD_NAME(kFindInteractionsWithinBlocksVdw, _kernel)(unsigned
...
@@ -108,9 +108,9 @@ __global__ void METHOD_NAME(kFindInteractionsWithinBlocksVdw, _kernel)(unsigned
float
dy
=
apos
.
y
-
center
.
y
;
float
dy
=
apos
.
y
-
center
.
y
;
float
dz
=
apos
.
z
-
center
.
z
;
float
dz
=
apos
.
z
-
center
.
z
;
#ifdef USE_PERIODIC
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dx
-=
floor
f
(
dx
*
cSim
.
invPeriodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dy
-=
floor
f
(
dy
*
cSim
.
invPeriodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
dz
-=
floor
f
(
dz
*
cSim
.
invPeriodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
#endif
dx
=
max
(
0
.
0
f
,
abs
(
dx
)
-
boxSize
.
x
);
dx
=
max
(
0
.
0
f
,
abs
(
dx
)
-
boxSize
.
x
);
dy
=
max
(
0
.
0
f
,
abs
(
dy
)
-
boxSize
.
y
);
dy
=
max
(
0
.
0
f
,
abs
(
dy
)
-
boxSize
.
y
);
...
...
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateCDLJObcGbsaSoftcoreForces1.h
View file @
470c9b7f
...
@@ -113,12 +113,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -113,12 +113,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dx
-=
floor
f
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dy
-=
floor
f
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
dz
-=
floor
f
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
invR
=
1
.
0
f
/
sqrt
(
r2
);
float
invR
=
1
.
0
f
/
sqrt
f
(
r2
);
float
sig
=
a
.
x
+
psA
[
j
].
sig
;
float
sig
=
a
.
x
+
psA
[
j
].
sig
;
float
eps
=
a
.
y
*
psA
[
j
].
eps
;
float
eps
=
a
.
y
*
psA
[
j
].
eps
;
#ifdef USE_SOFTCORE_LJ
#ifdef USE_SOFTCORE_LJ
...
@@ -147,9 +147,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -147,9 +147,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
// ObcGbsaForce1 part
// ObcGbsaForce1 part
float
alpha2_ij
=
br
*
psA
[
j
].
br
;
float
alpha2_ij
=
br
*
psA
[
j
].
br
;
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
expTerm
=
exp
(
-
D_ij
);
float
expTerm
=
exp
f
(
-
D_ij
);
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator
=
sqrt
(
denominator2
);
float
denominator
=
sqrt
f
(
denominator2
);
float
Gpol
=
(
q2
*
psA
[
j
].
q
)
/
(
denominator
*
denominator2
);
float
Gpol
=
(
q2
*
psA
[
j
].
q
)
/
(
denominator
*
denominator2
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
...
@@ -190,12 +190,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -190,12 +190,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dx
-=
floor
f
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dy
-=
floor
f
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
dz
-=
floor
f
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
invR
=
1
.
0
f
/
sqrt
(
r2
);
float
invR
=
1
.
0
f
/
sqrt
f
(
r2
);
float
sig
=
a
.
x
+
psA
[
j
].
sig
;
float
sig
=
a
.
x
+
psA
[
j
].
sig
;
float
eps
=
a
.
y
*
psA
[
j
].
eps
;
float
eps
=
a
.
y
*
psA
[
j
].
eps
;
...
@@ -235,9 +235,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -235,9 +235,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
alpha2_ij
=
br
*
psA
[
j
].
br
;
float
alpha2_ij
=
br
*
psA
[
j
].
br
;
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
expTerm
=
exp
(
-
D_ij
);
float
expTerm
=
exp
f
(
-
D_ij
);
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator
=
sqrt
(
denominator2
);
float
denominator
=
sqrt
f
(
denominator2
);
float
Gpol
=
(
q2
*
psA
[
j
].
q
)
/
(
denominator
*
denominator2
);
float
Gpol
=
(
q2
*
psA
[
j
].
q
)
/
(
denominator
*
denominator2
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
...
@@ -333,12 +333,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -333,12 +333,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
dy
=
psA
[
tj
].
y
-
apos
.
y
;
float
dy
=
psA
[
tj
].
y
-
apos
.
y
;
float
dz
=
psA
[
tj
].
z
-
apos
.
z
;
float
dz
=
psA
[
tj
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dx
-=
floor
f
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dy
-=
floor
f
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
dz
-=
floor
f
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
invR
=
1
.
0
f
/
sqrt
(
r2
);
float
invR
=
1
.
0
f
/
sqrt
f
(
r2
);
float
sig
=
a
.
x
+
psA
[
tj
].
sig
;
float
sig
=
a
.
x
+
psA
[
tj
].
sig
;
float
eps
=
a
.
y
*
psA
[
tj
].
eps
;
float
eps
=
a
.
y
*
psA
[
tj
].
eps
;
...
@@ -367,9 +367,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -367,9 +367,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
alpha2_ij
=
br
*
psA
[
tj
].
br
;
float
alpha2_ij
=
br
*
psA
[
tj
].
br
;
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
expTerm
=
exp
(
-
D_ij
);
float
expTerm
=
exp
f
(
-
D_ij
);
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator
=
sqrt
(
denominator2
);
float
denominator
=
sqrt
f
(
denominator2
);
float
Gpol
=
(
q2
*
psA
[
tj
].
q
)
/
(
denominator
*
denominator2
);
float
Gpol
=
(
q2
*
psA
[
tj
].
q
)
/
(
denominator
*
denominator2
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
...
@@ -418,12 +418,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -418,12 +418,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dx
-=
floor
f
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dy
-=
floor
f
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
dz
-=
floor
f
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
invR
=
1
.
0
f
/
sqrt
(
r2
);
float
invR
=
1
.
0
f
/
sqrt
f
(
r2
);
float
sig
=
a
.
x
+
psA
[
j
].
sig
;
float
sig
=
a
.
x
+
psA
[
j
].
sig
;
float
eps
=
a
.
y
*
psA
[
j
].
eps
;
float
eps
=
a
.
y
*
psA
[
j
].
eps
;
#ifdef USE_SOFTCORE_LJ
#ifdef USE_SOFTCORE_LJ
...
@@ -451,9 +451,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -451,9 +451,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
// ObcGbsaForce1 part
// ObcGbsaForce1 part
float
alpha2_ij
=
br
*
psA
[
j
].
br
;
float
alpha2_ij
=
br
*
psA
[
j
].
br
;
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
expTerm
=
exp
(
-
D_ij
);
float
expTerm
=
exp
f
(
-
D_ij
);
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator
=
sqrt
(
denominator2
);
float
denominator
=
sqrt
f
(
denominator2
);
float
Gpol
=
(
q2
*
psA
[
j
].
q
)
/
(
denominator
*
denominator2
);
float
Gpol
=
(
q2
*
psA
[
j
].
q
)
/
(
denominator
*
denominator2
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
...
@@ -544,12 +544,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -544,12 +544,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
dy
=
psA
[
tj
].
y
-
apos
.
y
;
float
dy
=
psA
[
tj
].
y
-
apos
.
y
;
float
dz
=
psA
[
tj
].
z
-
apos
.
z
;
float
dz
=
psA
[
tj
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dx
-=
floor
f
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dy
-=
floor
f
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
dz
-=
floor
f
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
invR
=
1
.
0
f
/
sqrt
(
r2
);
float
invR
=
1
.
0
f
/
sqrt
f
(
r2
);
float
sig
=
a
.
x
+
psA
[
tj
].
sig
;
float
sig
=
a
.
x
+
psA
[
tj
].
sig
;
float
eps
=
a
.
y
*
psA
[
tj
].
eps
;
float
eps
=
a
.
y
*
psA
[
tj
].
eps
;
#ifdef USE_SOFTCORE_LJ
#ifdef USE_SOFTCORE_LJ
...
@@ -582,9 +582,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
...
@@ -582,9 +582,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsaSoftcore, Forces1_kernel)(unsigned int* wo
float
alpha2_ij
=
br
*
psA
[
tj
].
br
;
float
alpha2_ij
=
br
*
psA
[
tj
].
br
;
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
D_ij
=
r2
/
(
4
.
0
f
*
alpha2_ij
);
float
expTerm
=
exp
(
-
D_ij
);
float
expTerm
=
exp
f
(
-
D_ij
);
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator2
=
r2
+
alpha2_ij
*
expTerm
;
float
denominator
=
sqrt
(
denominator2
);
float
denominator
=
sqrt
f
(
denominator2
);
float
Gpol
=
(
q2
*
psA
[
tj
].
q
)
/
(
denominator
*
denominator2
);
float
Gpol
=
(
q2
*
psA
[
tj
].
q
)
/
(
denominator
*
denominator2
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
float
dGpol_dalpha2_ij
=
-
0
.
5
f
*
Gpol
*
expTerm
*
(
1
.
0
f
+
D_ij
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
dEdR
+=
Gpol
*
(
1
.
0
f
-
0
.
25
f
*
expTerm
);
...
...
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